I am performing PCA in R and I got top 10 measurements (genes) that contribute for PC1:
loading_scores <- pca$rotation[,1]
gene_scores <- abs(loading_scores) ## get the magnitudes
gene_score_ranked <- sort(gene_scores, decreasing=TRUE)
top_10_genes <- names(gene_score_ranked[1:10])
top_10_genes
output:
[1] "ENSG00000169018.5" "ENSG00000181038.13" "ENSG00000103275.18" "ENSG00000174796.12"
[5] "ENSG00000164087.7"
How can I convert the ouputs from "gene IDs" into gene symbols? so that the outputs be like:
FEM1B
METTL23
UBE2I
etc..
Thanks in advance
Hello, please check my answer, here: Translating gene names to entrez id's
Note that you will need to remove those numerical suffixes from the Ensembl gene IDs
I run the first command:
library(org.Hs.eg.db)
mapIds(
org.Hs.eg.db,
keys = genes,
column = 'ENTREZID',
keytype = 'SYMBOL')
select(
org.Hs.eg.db,
keys = genes,
column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
keytype = 'SYMBOL')
But I still cant convert the extracted genesIDs to the symbols? How related to that code? Where I should put top_10_genes?
Thanks for answering
require(org.Hs.eg.db)
mapIds(
org.Hs.eg.db,
keys = genes,
column = 'SYMBOL',
keytype = 'ENSEMBL')
select(
org.Hs.eg.db,
keys = genes,
column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
keytype = 'ENSEMBL')
I have provided enough information such that you should be able to adapt my code to your own code. Please review my answer via the other link, to help you understand.
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for humans, use org.hs.eg.db
yes for humans, but how?